Methods Article
published: 26 August 2010 doi: 10.3389/fncir.2010.00100
NEURAL CIRCUITS
Ephus: multipurpose data acquisition software for neuroscience experiments Benjamin A. Suter 1, Timothy O’Connor 1, Vijay Iyer 2, Leopoldo T. Petreanu 2, Bryan M. Hooks 2, Taro Kiritani 1, Karel Svoboda 2 and Gordon M. G. Shepherd 1,2* Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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Edited by: Giorgio Ascoli, George Mason University, USA Reviewed by: German Barrionuevo, University of Pittsburgh, USA Xiangmin Xu, University of California at Irvine, USA *Correspondence: Gordon M. G. Shepherd, Department of Physiology, Feinberg School of Medicine, Northwestern University, Morton 5-660, 303 East Chicago Avenue, Chicago, IL 60611, USA. e-mail:
[email protected]
Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications. Keywords: software, data acquisition, electrophysiology, mapping, imaging
Introduction Software tools are crucial for neuroscience experiments involving complex combinations of event-driven stimulus and recording paradigms. Although commercial software solutions exist, these are often limited by a variety of factors including cost, source code inaccessibility, hardware compatibility, and more. Consequently a strong tradition in neurophysiology research is to write custom software routines. While superb for the specific tasks at hand, these custom solutions rarely offer the flexibility and extensibility needed for them to be transferrable across platforms, hardware configurations, and experimental paradigms without significant modifications. We present here a suite of software tools engineered around general-purpose data I/O. This package, Ephus, is module-based and includes functionality for a wide variety of applications ranging from traditional in vitro electrophysiology to highly customized circuit mapping and in vivo behavioral protocols. Ephus has evolved alongside ScanImage, a package dedicated for 2-photon laser scanning microscopy (Pologruto et al., 2003). Ephus offers a collection of both application-specific tools, such as those for electrophysiology, scanning and mapping, video imaging, as well as common (shared) tools for data binding, configuration switching, and experimental timing. Ephus has been used for standard cellular electrophysiology, synaptic circuit mapping using laser scanning photostimulation (LSPS), and electrophysiology in vivo behavioral paradigms, and it offers a wide range of potential applications: whole-cell recording with non-standard customized routines including multi-electrode Abbreviations and Conventions: AD, analog-to-digital; DA, digital-to-analog; DIO – digital I/O; I/O, input/output; Italics, Ephus modules and programs are in italics: e.g., stimulator.
Frontiers in Neural Circuits
applications; complex combinations of multiple I/O devices and signals; uncaging and optogenetic based synaptic mapping applications; and, event-driven in vivo behavioral experiments. Parts of this work have been published in preliminary format (O’Connor et al., 2008, 2009).
Methods Web site
The Ephus web address is http://www.ephus.org. The site includes links for downloading Ephus and related tools, and extensive information about installation, configuration, and usage. Feedback can be provided as well (
[email protected]). Software development
Ephus was developed and tested on multiple computers (Dell, Lenovo, Superlogics) running Microsoft Windows XP. Setting up hardware and ancillary software
Matlab and ancillary software
Ephus runs within Matlab (version 2007b and higher; Mathworks, Natick, MA, USA) as a series of scripts, classes, and custom toolboxes. No commercial Matlab toolboxes are required. Data acquisition is through NiMex, a custom toolbox which is included in Ephus. GLib, an open-source, cross-platform utility library, is automatically installed. Computer
The Ephus computer must accommodate the data acquisition boards (via PCI/PCIe slots or USB connectors, as appropriate) and, where needed, a video camera (usually an IEEE 1394 interface connection).
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Ephus software
Data acquisition boards
Multiple levels of customization
National Instruments (NI; Austin, TX, USA) data acquisition boards are supported (AO, E, and M series). NI driver version NI-DAQmx 8.5.05 or higher is recommended. For electrophysiology and mapping experiments boards such as the following are often used: PCI/USB-6229 and -6259; PCI-6040E; PCI-6713. The number and type depends on the number of channels required. Note that Ephus, through NiMex, is able to support precision-timed DIO (“correlated DIO” in NI terminology). This greatly expands the number of available data I/O channels available.
Ephus allows easy configuration and display of individual experimental parameters via controls on the graphical user interface (window) for the various programs. However, Ephus also allows rapid ( arcuate nucleus microcircuits and their reorganization by fasting. Nat. Neurosci. 8, 1356–1363. Theyel, B. B., Llano, D. A., and Sherman, S. M. (2010). The corticothalamocortical circuit drives higher-order cortex in the mouse. Nat. Neurosci. 13, 84–88. Weiler, N., Wood, L., Yu, J., Solla, S. A., and Shepherd, G. M. G. (2008). Topdown laminar organization of the excitatory network in motor cortex. Nat. Neurosci. 11, 360–366. Wood, L., Gray, N. W., Zhou, Z., Greenberg, M. E., and Shepherd, G. M. (2009). Synaptic circuit abnormalities of motor-frontal layer 2/3 pyramidal neurons in an RNA interference model of methyl-CpG-binding protein 2 deficiency. J. Neurosci. 29, 12440–12448. Wood, L., and Shepherd, G. M. (2010). Synaptic circuit abnormalities of motorfrontal layer 2/3 pyramidal neurons in a mutant mouse model of Rett syndrome. Neurobiol. Dis. 38, 281–287. Xu, X., Olivas, N. D., Levi, R., Ikrar, T., and Nenadic, Z. (2010). High precision and fast functional mapping of cortical circuitry through a novel combination of voltage sensitive dye imaging and laser scanning photostimulation. J. Neurophysiol. 103, 2301–2312. Yourdon, E., and Constantine, L. L. (1979). Structured Design: Fundamentals of a Discipline of Computer Program and System Design. Upper Saddle River, NJ: Prentice-Hall. Yu, J., Anderson, C. T., Kiritani, T., Sheets, P. L., Wokosin, D. L., Wood, L., and Shepherd, G. M. (2008). Local-circuit phenotypes of layer 5 neurons in motor-frontal cortex of YFP-H mice. Front. Neural. Circuits 2:6. doi:10.3389/ neuro.04.006.2008. Zhao, C., Kao, J. P., and Kanold, P. O. (2009). Functional excitatory
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icrocircuits in neonatal cortex conm nect thalamus and layer 4. J. Neurosci. 29, 15479–15488. Zito, K., Knott, G., Shepherd, G. M., Shenolikar, S., and Svoboda, K. (2004). Induction of spine growth and synapse formation by regulation of the spine actin cytoskeleton. Neuron 44, 321–334.
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Ephus software
Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Received: 18 April 2010; Paper pending published: 18 May 2010; accepted: 01
July 2010; published online: 26 August 2010. Citation: Suter BA, O’Connor T, Iyer V, Petreanu LT, Hooks BM, Kiritani T, Svoboda K and Shepherd GMG (2010) Ephus: multipurpose data acquisition software for neuroscience experiments. Front. Neural Circuits 4:100. doi: 10.3389/fncir.2010.00100
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Copyright © 2010 Suter, O’Connor, Iyer, Petreanu, Hooks, Kiritani, Svoboda and Shepherd. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
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